prada (version 1.48.0)

threePanelPlot: Visualize cytometry data

Description

Function to visualize multivariate (cytometry) data in three two-dimensional plots.

Usage

threePanelPlot(data, x.panels = c(1, 4, 5), y.panels = c(2, 3, 6), tot.width = 15, tot.height = 5.4, maxcells = 20000, limits = c(0, 1023), remove.extremes = TRUE, plotTitle = "Three-Panel Plot", use.smoothScatter = TRUE, palette = colorRampPalette(brewer.pal(9, "Blues")), new.device = TRUE, verbose = TRUE, addPoints = NULL, addCol = "red", ...)

Arguments

data

data matrix to visualize

x.panels

which variables (columns) are to be plotted at the x-axis of the three variables

y.panels

which variables (columns) are to be plotted at the y-axis of the three variables

tot.width

width of a new device to open, see argument new.device

tot.height

height of a new device to open, see argument new.device

maxcells

maximum number of observations (cells) for plotting; higher numbers reduce performance

limits

minimum and maximum value (theoretically) observed in the data; e.g., with 10-channel digitized data it is c(0,1023)

remove.extremes

logical; are extreme values (equal to theoretical limits) to be removed before plotting

plotTitle

title for the plot

use.smoothScatter

logical, should the function smoothScatter be employed for plotting the data (plots data densities rather than individual points)

palette

if smoothScatter is used, which colour palette is it to use

new.device

logical; should a new device be opened for the three plots; if FALSE the three plots will be plotted to the currently active device

verbose

logical; do you want extended output to STDOUT

addPoints

should special points be marked after plotting the data; is expected to be a subser of argument data with the same number of columns (=variables); if NULL no points are marked

addCol

in which colour are the points in addPoints to be marked

...

further arguments passed on to plot.default

Value

no value is returned; the function is called to produce three plots

See Also

plot.default

Examples

   # generate some data:
   toyData <- cbind(matrix(pmax(0,pmin(runif(3000)+rnorm(3000),4)),ncol=3),
                    matrix(pmax(0,pmin(rnorm(3000,2,1),4)),ncol=3))
   colnames(toyData) <- paste("Var",1:6,sep="")
   toyQuantiles <- apply(toyData,2,quantile,probs=c(0.25,0.5,0.75))

   # plot it and mark the quantiles:
   threePanelPlot(toyData,addPoints=toyQuantiles,
                  addCol=c("orange","red","purple"),limits=c(0,4),pch=20)